If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ), 'gf_id' => 'HOM05D001078', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001078' ), 'data_identifier' => 'HOM05D001078', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001078', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '569', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p16670' => 'bna', 'A07p15530' => 'bna', 'A07p42000' => 'bna', 'A08p29290' => 'bna', 'Aa31LG3G10930' => 'aar', 'Aa31LG4G6450' => 'aar', 'Aa31LG7G4880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.693' => 'aag', 'Actinidia05089' => 'ach', 'Actinidia10740' => 'ach', 'Actinidia11478' => 'ach', 'Actinidia11638' => 'ach', 'Actinidia15503' => 'ach', 'Actinidia16362' => 'ach', 'Actinidia17053' => 'ach', 'Actinidia17996' => 'ach', 'Actinidia20573' => 'ach', 'Actinidia23149' => 'ach', 'Actinidia24794' => 'ach', 'Actinidia24795' => 'ach', 'Actinidia28608' => 'ach', 'Actinidia35357' => 'ach', 'Actinidia37915' => 'ach', 'Ah.00g000970' => 'amhyb', 'Ah.01g010000' => 'amhyb', 'Ah.04g165980' => 'amhyb', 'Ah.15g089780' => 'amhyb', 'AL1G33640' => 'aly', 'AL2G36480' => 'aly', 'AL8G30520' => 'aly', 'Aqoxy1G00181' => 'aox', 'Aqoxy1G02099' => 'aox', 'Aqoxy5G01017' => 'aox', 'Aqoxy6G01630' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CUFW55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CZ315L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F4DV7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HE6943' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J18WU7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KDCW8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2IIWY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R0BHUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8BZZJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WT4A18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8B0E4' => 'arhy', 'AT1G20670' => 'ath', 'AT1G76380' => 'ath', 'AT5G55040' => 'ath', 'ATR0794G116' => 'atr', 'ATR0807G235' => 'atr', 'ATR1127G001' => 'atr', 'Atru.chr13.122' => 'acertr', 'Atru.chr13.123' => 'acertr', 'Atru.chr2.3452' => 'acertr', 'Atru.chr5.3539' => 'acertr', 'Atru.chr5.3540' => 'acertr', 'Atru.chr8.58' => 'acertr', 'AUR62006454' => 'cqu', 'AUR62010168' => 'cqu', 'AUR62013169' => 'cqu', 'AUR62015795' => 'cqu', 'AUR62020421' => 'cqu', 'AUR62029810' => 'cqu', 'AUR62035129' => 'cqu', 'AUR62040819' => 'cqu', 'BcaB03g12858' => 'bca', 'BcaB03g14308' => 'bca', 'BcaB07g32064' => 'bca', 'BcaB07g32067' => 'bca', 'BcaC05g25977' => 'bca', 'BcaC06g34828' => 'bca', 'BcaC07g39048' => 'bca', 'BcaC08g47135' => 'bca', 'BcaC08g47257' => 'bca', 'BolC5t30629H' => 'bol', 'BolC6t40082H' => 'bol', 'BolC7t42829H' => 'bol', 'BolC8t49659H' => 'bol', 'BraA06t24774Z' => 'bra', 'BraA07t29294Z' => 'bra', 'BraA07t31730Z' => 'bra', 'BraA08t34864Z' => 'bra', 'C05p19290' => 'bna', 'C06p50570' => 'bna', 'C07p22900' => 'bna', 'C08p20310' => 'bna', 'CAN.G110.5' => 'can', 'CAN.G110.6' => 'can', 'CAN.G110.7' => 'can', 'CAN.G110.8' => 'can', 'CAN.G311.128' => 'can', 'CAN.G337.81' => 'can', 'CAN.G4246.1' => 'can', 'CANSAT11G0386' => 'cansat', 'CANSAT25G1838' => 'cansat', 'CANSAT25G2030' => 'cansat', 'CANSAT54G2443' => 'cansat', 'CANSAT56G1972' => 'cansat', 'CARHR021120' => 'chi', 'CARHR069930' => 'chi', 'CARHR268360' => 'chi', 'Carub.0001s2014' => 'cru', 'Carub.0002s2328' => 'cru', 'Carub.0008s1531' => 'cru', 'Ca_05730_v3' => 'car', 'Ca_06328_v3' => 'car', 'Ca_15412_v3' => 'car', 'Ca_23105_v3' => 'car', 'Ca_27043_v3' => 'car', 'Ca_30699_v3' => 'car', 'CBR_g37121' => 'cbr', 'Cc00_g18580' => 'ccan', 'Cc00_g24760' => 'ccan', 'Cc05_g13930' => 'ccan', 'Cc06_g00160' => 'ccan', 'CDE05G1337' => 'cde', 'CDE05G1366' => 'cde', 'CDE06G0304' => 'cde', 'CDE06G1472' => 'cde', 'CDE06G2679' => 'cde', 'Cfa011858' => 'cfa', 'Cfa014099' => 'cfa', 'Cfa020326' => 'cfa', 'Cfa025964' => 'cfa', 'Ciclev10000481m.g' => 'ccl', 'Ciclev10007654m.g' => 'ccl', 'Ciclev10013126m.g' => 'ccl', 'Ciclev10013346m.g' => 'ccl', 'Ciclev10027882m.g' => 'ccl', 'CiPaw.05G092400' => 'cil', 'CiPaw.06G116000' => 'cil', 'CiPaw.07G137000' => 'cil', 'CiPaw.08G074500' => 'cil', 'CiPaw.11G191200' => 'cil', 'CiPaw.12G131000' => 'cil', 'CiPaw.13G060100' => 'cil', 'CiPaw.13G060200' => 'cil', 'ClCG02G003450' => 'cla', 'ClCG09G010860' => 'cla', 'ClCG11G018770' => 'cla', 'COL.COLO4_06159' => 'col', 'COL.COLO4_09674' => 'col', 'COL.COLO4_19498' => 'col', 'COL.COLO4_34299' => 'col', 'COL.COLO4_36411' => 'col', 'Cpa.g.sc0.55' => 'cpa', 'Cpa.g.sc12.290' => 'cpa', 'Cpa.g.sc12.291' => 'cpa', 'Cpa.g.sc19.71' => 'cpa', 'Cpa.g.sc26.181' => 'cpa', 'Cre04.g225950' => 'cre', 'Cre17.g711100' => 'cre', 'CsaV3_4G037340' => 'csa', 'CsaV3_7G001860' => 'csa', 'CsaV3_7G021900' => 'csa', 'CSS0004498' => 'camsi', 'CSS0006773' => 'camsi', 'CSS0011918' => 'camsi', 'CSS0012271' => 'camsi', 'CSS0032528' => 'camsi', 'CSS0032667' => 'camsi', 'CSS0032882' => 'camsi', 'CSS0042555' => 'camsi', 'CSS0043187' => 'camsi', 'DCAR_013928' => 'dca', 'DCAR_016713' => 'dca', 'DCAR_016779' => 'dca', 'Dinv12294' => 'din', 'Dinv14171' => 'din', 'Dinv16935' => 'din', 'Dinv17072' => 'din', 'Dinv22255' => 'din', 'Dinv28759' => 'din', 'Dinv31956' => 'din', 'Dinv40767' => 'din', 'Dinv41873' => 'din', 'Dinv43016' => 'din', 'Dinv43081' => 'din', 'Dinv44215' => 'din', 'Duzib052G0460' => 'dzi', 'Duzib093G1480' => 'dzi', 'Duzib114G0176' => 'dzi', 'Duzib114G0613' => 'dzi', 'Duzib116G0459' => 'dzi', 'Duzib132G1240' => 'dzi', 'Duzib151G0405' => 'dzi', 'Duzib213G0265' => 'dzi', 'Duzib248G0426' => 'dzi', 'ECA233G1484' => 'eca', 'ECA238G1763' => 'eca', 'ECA246G0232' => 'eca', 'EL10Ac1g01923' => 'bvu', 'EL10Ac4g07787' => 'bvu', 'EL10Ac7g17142' => 'bvu', 'EL10Ac9g21524' => 'bvu', 'Eucgr.F00750' => 'egr', 'Eucgr.F03477' => 'egr', 'Eucgr.F03569' => 'egr', 'Eucgr.I01525' => 'egr', 'FAN01G0123' => 'fan', 'FAN02G1981' => 'fan', 'FAN03G1112' => 'fan', 'FAN04G2862' => 'fan', 'FAN05G4732' => 'fan', 'FAN08G2729' => 'fan', 'FAN09G3692' => 'fan', 'FAN11G3397' => 'fan', 'FAN11G3507' => 'fan', 'FAN13G2693' => 'fan', 'FAN14G3499' => 'fan', 'FAN15G1398' => 'fan', 'FAN16G1957' => 'fan', 'FAN16G3411' => 'fan', 'FAN18G1695' => 'fan', 'FAN21G1617' => 'fan', 'FAN21G1620' => 'fan', 'FAN24G1793' => 'fan', 'FAN25G0643' => 'fan', 'FAN25G2972' => 'fan', 'FAN25G3400' => 'fan', 'FAN27G1847' => 'fan', 'FvH4_2g16690' => 'fve', 'FvH4_3g22980' => 'fve', 'FvH4_3g41110' => 'fve', 'FvH4_5g24560' => 'fve', 'FvH4_5g25400' => 'fve', 'FvH4_6g09360' => 'fve', 'FvH4_7g04861' => 'fve', 'FvH4_7g26330' => 'fve', 'Glyma.02G189250' => 'gma', 'Glyma.04G016900' => 'gma', 'Glyma.06G017300' => 'gma', 'Glyma.08G318100' => 'gma', 'Glyma.08G318200' => 'gma', 'Glyma.11G201000' => 'gma', 'Glyma.13G066200' => 'gma', 'Glyma.14G022600' => 'gma', 'Glyma.16G221600' => 'gma', 'Glyma.18G050000' => 'gma', 'Glyma.18G095200' => 'gma', 'Glyma.18G095400' => 'gma', 'Gohir.A02G001100' => 'ghi', 'Gohir.A02G085100' => 'ghi', 'Gohir.A04G014100' => 'ghi', 'Gohir.A05G178600' => 'ghi', 'Gohir.A05G178700' => 'ghi', 'Gohir.A05G178800' => 'ghi', 'Gohir.A05G178900' => 'ghi', 'Gohir.A12G013300' => 'ghi', 'Gohir.D02G001400' => 'ghi', 'Gohir.D02G100800' => 'ghi', 'Gohir.D05G181900' => 'ghi', 'Gohir.D05G182000' => 'ghi', 'Gohir.D05G182100' => 'ghi', 'Gohir.D05G372200' => 'ghi', 'Gohir.D12G014100' => 'ghi', 'Gorai.005G001900' => 'gra', 'Gorai.005G114300' => 'gra', 'Gorai.008G014100' => 'gra', 'Gorai.009G187000' => 'gra', 'Gorai.009G187100' => 'gra', 'Gorai.009G187200' => 'gra', 'Gorai.009G187300' => 'gra', 'Gorai.009G187400' => 'gra', 'Gorai.009G440400' => 'gra', 'Gorai.012G012700' => 'gra', 'GSVIVG01013381001' => 'vvi', 'GSVIVG01024528001' => 'vvi', 'GSVIVG01029855001' => 'vvi', 'GSVIVG01037668001' => 'vvi', 'GSVIVG01037669001' => 'vvi', 'HanXRQChr05g0139441' => 'han', 'HanXRQChr05g0159511' => 'han', 'HanXRQChr06g0184151' => 'han', 'HanXRQChr13g0417951' => 'han', 'HanXRQChr14g0427621' => 'han', 'HanXRQChr16g0504791' => 'han', 'Haze_02008' => 'cav', 'Haze_02009' => 'cav', 'Haze_09697' => 'cav', 'Haze_16656' => 'cav', 'Haze_21209' => 'cav', 'Haze_22813' => 'cav', 'Haze_22815' => 'cav', 'Haze_24492' => 'cav', 'Hma1.2p1_0175F.1_g077080' => 'hma', 'Hma1.2p1_0507F.1_g168670' => 'hma', 'HPP92_007116' => 'vpl', 'HPP92_014179' => 'vpl', 'HPP92_014180' => 'vpl', 'HPP92_014559' => 'vpl', 'HPP92_025505' => 'vpl', 'HPP92_025530' => 'vpl', 'Hund00077' => 'sun', 'Hund06367' => 'sun', 'Hund23234' => 'sun', 'Hund28571' => 'sun', 'Hund28574' => 'sun', 'Lalb_Chr01g0016431' => 'lal', 'Lalb_Chr04g0251611' => 'lal', 'Lalb_Chr08g0246471' => 'lal', 'Lalb_Chr13g0290341' => 'lal', 'Lalb_Chr14g0370661' => 'lal', 'Lalb_Chr15g0085621' => 'lal', 'Lalb_Chr17g0348511' => 'lal', 'Lalb_Chr23g0265711' => 'lal', 'Lj1g0019508' => 'lja', 'Lj2A1105T51' => 'lonja', 'Lj2A1107G66' => 'lonja', 'Lj2A1126T35' => 'lonja', 'Lj2C1105T10' => 'lonja', 'Lj2C1105T11' => 'lonja', 'Lj2C55G8' => 'lonja', 'Lj3g0000933' => 'lja', 'Lj3g0011258' => 'lja', 'Lj4C807T5' => 'lonja', 'Lj4C8G3' => 'lonja', 'Lj5A172T83' => 'lonja', 'Lj6g0014414' => 'lja', 'Lj8A170G78' => 'lonja', 'Lj8A170G79' => 'lonja', 'LjContig00141g0013234' => 'lja', 'LjContig00272g0005281' => 'lja', 'Lsat_1_v5_gn_2_3480' => 'lsa', 'Lsat_1_v5_gn_5_3721' => 'lsa', 'Lsat_1_v5_gn_8_25780' => 'lsa', 'Lsat_1_v5_gn_9_39821' => 'lsa', 'Lsat_1_v5_gn_9_45480' => 'lsa', 'Manes.02G002700' => 'mes', 'Manes.02G208700' => 'mes', 'Manes.03G131100' => 'mes', 'Manes.03G131200' => 'mes', 'Manes.04G067000' => 'mes', 'Manes.05G123900' => 'mes', 'Manes.08G167600' => 'mes', 'Manes.11G110400' => 'mes', 'Manes.18G124000' => 'mes', 'Mapoly0004s0082' => 'mpo', 'Mapoly0072s0016' => 'mpo', 'Mapoly0250s0003' => 'mpo', 'MBI05_g09440_MAGBIO' => 'mbi', 'MBI08_g12263_MAGBIO' => 'mbi', 'MBI08_g26558_MAGBIO' => 'mbi', 'MBI08_g41022_MAGBIO' => 'mbi', 'MBI08_g41023_MAGBIO' => 'mbi', 'MBI15_g31021_MAGBIO' => 'mbi', 'MBI18_g06103_MAGBIO' => 'mbi', 'MD01G1172400' => 'mdo', 'MD03G1199100' => 'mdo', 'MD04G1178300' => 'mdo', 'MD05G1135100' => 'mdo', 'MD06G1010000' => 'mdo', 'MD07G1238700' => 'mdo', 'MD10G1140600' => 'mdo', 'MD11G1215500' => 'mdo', 'MD16G1284400' => 'mdo', 'Medtr3g052530' => 'mtr', 'Medtr3g115560' => 'mtr', 'Medtr3g463230' => 'mtr', 'Medtr5g075950' => 'mtr', 'Medtr5g093070' => 'mtr', 'Medtr8g005100' => 'mtr', 'MELO3C013156.2' => 'cme', 'MELO3C013253.2' => 'cme', 'MELO3C017030.2' => 'cme', 'MELO3C027396.2' => 'cme', 'Migut.H01816' => 'egut', 'Migut.J00009' => 'egut', 'Migut.M01747' => 'egut', 'Migut.M01761' => 'egut', 'Migut.N02966' => 'egut', 'Migut.O00320' => 'egut', 'MSTRG.12982' => 'ama', 'MSTRG.14439' => 'ama', 'MSTRG.15137' => 'ama', 'MSTRG.22095' => 'ama', 'MSTRG.24499' => 'ama', 'Nitab4.5_0000195g0020' => 'nta', 'Nitab4.5_0000486g0220' => 'nta', 'Nitab4.5_0002287g0090' => 'nta', 'Nitab4.5_0004009g0020' => 'nta', 'Nitab4.5_0004356g0030' => 'nta', 'Nitab4.5_0004470g0050' => 'nta', 'Nitab4.5_0005590g0030' => 'nta', 'Nn1g03501' => 'nnu', 'Nn1g07159' => 'nnu', 'Nn5g26777' => 'nnu', 'Oeu013140.1' => 'oeu', 'Oeu027180.1' => 'oeu', 'Oeu036912.1' => 'oeu', 'Oeu042944.1' => 'oeu', 'Oeu062585.1' => 'oeu', 'Os07g0511900' => 'osa', 'Os09g0550000' => 'osa', 'Peaxi162Scf00235g00321' => 'pax', 'Peaxi162Scf00501g00610' => 'pax', 'Peaxi162Scf00711g00113' => 'pax', 'Peaxi162Scf00732g00114' => 'pax', 'PGR031G0080' => 'pgr', 'PGR031G1450' => 'pgr', 'PGR031G3104' => 'pgr', 'PGR031G3827' => 'pgr', 'PGR031G3838' => 'pgr', 'PGR083G1710' => 'pgr', 'PGR142G3568' => 'pgr', 'PGSC0003DMG400009988' => 'stu', 'PGSC0003DMG400015657' => 'stu', 'PGSC0003DMG400019814' => 'stu', 'PGSC0003DMG400022213' => 'stu', 'Phvul.006G045600' => 'pvu', 'Phvul.006G081200' => 'pvu', 'Phvul.006G081400' => 'pvu', 'Phvul.006G081500' => 'pvu', 'Phvul.008G268700' => 'pvu', 'Phvul.009G011800' => 'pvu', 'Phvul.010G059800' => 'pvu', 'Potri.002G009100' => 'ptr', 'Potri.004G206200' => 'ptr', 'Potri.005G252200' => 'ptr', 'Potri.006G112000' => 'ptr', 'Potri.009G167500' => 'ptr', 'Potri.016G141400' => 'ptr', 'Potri.019G132601' => 'ptr', 'Pp3c27_6220' => 'ppa', 'Pp3c5_1040' => 'ppa', 'Pp3c6_29000' => 'ppa', 'PRCOL_00001060' => 'pco', 'PRCOL_00006424' => 'pco', 'PRCOL_00006473' => 'pco', 'PRCOL_00007008' => 'pco', 'Prupe.2G267500' => 'ppe', 'Prupe.4G215800' => 'ppe', 'Prupe.5G010200' => 'ppe', 'Prupe.6G298300' => 'ppe', 'Prupe.8G179000' => 'ppe', 'Psat0s3486g0040' => 'psa', 'Psat2g011520' => 'psa', 'Psat5g010760' => 'psa', 'Psat5g176480' => 'psa', 'PSO210G0993' => 'pso', 'PSO210G2542' => 'pso', 'PSO339G0327' => 'pso', 'PSO384G3565' => 'pso', 'PSO541G1235' => 'pso', 'PSO541G2226' => 'pso', 'PSO675G7296' => 'pso', 'PSO675G8452' => 'pso', 'PSO761G0003' => 'pso', 'PSO832G3726' => 'pso', 'QL01p023694' => 'qlo', 'QL02p014681' => 'qlo', 'QL07p008165' => 'qlo', 'QL07p031378' => 'qlo', 'QL08p009613' => 'qlo', 'QL11p056167' => 'qlo', 'RcHm_v2.0_Chr1g0372791' => 'rch', 'RcHm_v2.0_Chr3g0459751' => 'rch', 'RcHm_v2.0_Chr5g0040321' => 'rch', 'RcHm_v2.0_Chr6g0280831' => 'rch', 'RcHm_v2.0_Chr7g0215631' => 'rch', 'Rhsim05G0233900' => 'rsi', 'Rhsim06G0006100' => 'rsi', 'Rhsim06G0218500' => 'rsi', 'Rhsim07G0256700' => 'rsi', 'RhsimUnG0249300' => 'rsi', 'Sabra02G0006700' => 'sbr', 'Sabra04G0157800' => 'sbr', 'Sabra05G0195600' => 'sbr', 'Sabra06G0087300' => 'sbr', 'Sabra19G0128900' => 'sbr', 'Sabra19G0129000' => 'sbr', 'SalBow6G3646' => 'sbo', 'SalBow7G3577' => 'sbo', 'Sc15g0004360' => 'sci', 'Sc15g0004370' => 'sci', 'Sc15g0004380' => 'sci', 'Sc16g0005940' => 'sci', 'Sc18g0005910' => 'sci', 'Sc20g0007290' => 'sci', 'Sc20g0007580' => 'sci', 'Sed0008760' => 'sed', 'Sed0011453' => 'sed', 'Sed0017255' => 'sed', 'Sed0021197' => 'sed', 'SEGI_18061' => 'sgi', 'SEGI_24250' => 'sgi', 'SEGI_30382' => 'sgi', 'SEGI_36302' => 'sgi', 'SEGI_41155' => 'sgi', 'SGA_v2.0_scaffold1091G53836' => 'sas', 'SGA_v2.0_scaffold235G43696' => 'sas', 'SGA_v2.0_scaffold364G49983' => 'sas', 'SGA_v2.0_scaffold373G50197' => 'sas', 'SGA_v2.0_scaffold43G16258' => 'sas', 'SGA_v2.0_scaffold54G19661' => 'sas', 'SGA_v2.0_scaffold8G04327' => 'sas', 'SHI07973' => 'shi', 'SHI26593' => 'shi', 'SMO304G0009' => 'smo', 'Solyc04g082530.3' => 'sly', 'Solyc06g051210.3' => 'sly', 'Solyc07g064700.4' => 'sly', 'Solyc09g055660.3' => 'sly', 'Sopen04g036150' => 'spe', 'Sopen06g017120' => 'spe', 'Sopen07g032900' => 'spe', 'Sopen09g018840' => 'spe', 'Sp1g18380' => 'spa', 'Sp5g31530' => 'spa', 'Sp6g16970' => 'spa', 'TAR376G0529' => 'tar', 'TAR381G0835' => 'tar', 'TAR623G1781' => 'tar', 'TAR624G0730' => 'tar', 'TAR626G0690' => 'tar', 'TAR627G0281' => 'tar', 'TAR628G1074' => 'tar', 'TAR633G1652' => 'tar', 'THA.LOC104809829' => 'tha', 'THA.LOC104811472' => 'tha', 'THA.LOC104811614' => 'tha', 'THA.LOC104813751' => 'tha', 'THA.LOC104827077' => 'tha', 'Thecc.02G135800' => 'tca', 'Thecc.02G145300' => 'tca', 'Thecc.03G220300' => 'tca', 'Thecc.04G146600' => 'tca', 'Thecc.07G033900' => 'tca', 'Thecc.08G061000' => 'tca', 'Thecc.08G061100' => 'tca', 'Thhalv10007011m.g' => 'esa', 'Thhalv10018318m.g' => 'esa', 'TPR.G1187' => 'tpr', 'TPR.G13277' => 'tpr', 'TPR.G23042' => 'tpr', 'TPR.G30728' => 'tpr', 'TPR.G33790' => 'tpr', 'TPR.G38084' => 'tpr', 'TWI12G1132' => 'twi', 'TWI31G0667' => 'twi', 'TWI36G0672' => 'twi', 'TWI38G0838' => 'twi', 'TWI38G1825' => 'twi', 'TWI39G0966' => 'twi', 'TWI53G1322' => 'twi', 'TWI56G0470' => 'twi', 'TWI63G0269' => 'twi', 'TWI79G1230' => 'twi', 'unitig_26.g9875' => 'ugi', 'unitig_32.g11162' => 'ugi', 'unitig_62.g23287' => 'ugi', 'unitig_744.g24085' => 'ugi', 'vmacro02227' => 'vma', 'vmacro04415' => 'vma', 'vmacro09702' => 'vma', 'vmacro20397' => 'vma', 'vmacro21800' => 'vma', 'VMungo0331G0009' => 'vmu', 'VMungo0540G0032' => 'vmu', 'VMungo0540G1541' => 'vmu', 'VMungo0647G0084' => 'vmu', 'VMungo1309G1094' => 'vmu', 'Zm00001eb002460' => 'zma', 'Zm00001eb015850' => 'zma', 'Zm00001eb104280' => 'zma', 'Zm00001eb105830' => 'zma', 'Zm00001eb320910' => 'zma', 'Zm00001eb322530' => 'zma', 'Zm00001eb402500' => 'zma' ) $gf_id = 'HOM05D001078' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001078' ) $data_identifier = 'HOM05D001078' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 15, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 12, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 22, 'fve' => (int) 8, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 6, 'cav' => (int) 8, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 6, 'lonja' => (int) 11, 'lsa' => (int) 5, 'mes' => (int) 9, 'mpo' => (int) 3, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 7, 'stu' => (int) 4, 'pvu' => (int) 7, 'ptr' => (int) 7, 'ppa' => (int) 3, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 7, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 5, 'tca' => (int) 7, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 10, 'ugi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402500' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1